Problem with blending 2 UV Maps with Tiled Textures with a 3rd Layer
Does something like this work for you? If you want to blend the textures, you can use gray instead of Black or White;

Different Shader on same label

Note: While this uses nodes in Blender, you should be able to blend textures in your game engine using a similar process, and the textures you create in blender would carry over.